Zinc in PDB 6oda: Crystal Structure of HDAC8 in Complex with Compound 2

All present enzymatic activity of Crystal Structure of HDAC8 in Complex with Compound 2:
3.5.1.98;

The structure of Crystal Structure of HDAC8 in Complex with Compound 2, PDB code: 6oda was solved by X.Zheng, C.Conti, J.Caravella, M.-M.Zablocki, K.Bair, N.Barczak, B.Han, D.Lancia Jr., C.Liu, M.Martin, P.Y.Ng, A.Rudnitskaya, J.J.Thomason, R.Garcia-Dancey, C.Hardy, J.Lahdenranta, C.Leng, P.Li, E.Pardo, A.Saldahna, T.Tan, A.V.Toms, L.Yao, C.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.750, 91.290, 92.700, 90.00, 94.09, 90.00
R / Rfree (%)	19.9 / 24.9

The structure of Crystal Structure of HDAC8 in Complex with Compound 2 also contains other interesting chemical elements:

Fluorine	(F)	9 atoms
Potassium	(K)	6 atoms

The binding sites of Zinc atom in the Crystal Structure of HDAC8 in Complex with Compound 2 (pdb code 6oda). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of HDAC8 in Complex with Compound 2, PDB code: 6oda:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of HDAC8 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of HDAC8 in Complex with Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:39.1 occ:1.00 OD2 A:ASP267 2.0 39.6 1.0 OAL A:C7401 2.0 53.7 1.0 OD1 A:ASP178 2.0 44.2 1.0 OAK A:C7401 2.0 55.5 1.0 ND1 A:HIS180 2.2 44.7 1.0 CAI A:C7401 2.7 65.5 1.0 NAJ A:C7401 2.7 60.3 1.0 CG A:ASP178 2.9 41.6 1.0 CG A:ASP267 3.1 37.4 1.0 CE1 A:HIS180 3.1 44.8 1.0 OD2 A:ASP178 3.2 41.5 1.0 CG A:HIS180 3.2 43.4 1.0 OD1 A:ASP267 3.5 37.5 1.0 CB A:HIS180 3.6 41.6 1.0 N A:HIS180 3.7 40.3 1.0 NE2 A:HIS180 4.2 44.4 1.0 CA A:GLY304 4.2 36.6 1.0 CAH A:C7401 4.2 75.8 1.0 CD2 A:HIS180 4.2 43.7 1.0 CA A:HIS180 4.3 40.8 1.0 N A:LEU179 4.3 39.9 1.0 CB A:ASP178 4.3 40.6 1.0 CB A:ASP267 4.4 37.4 1.0 CB A:LEU179 4.5 40.4 1.0 OH A:TYR306 4.6 39.0 1.0 NE2 A:HIS142 4.6 37.8 1.0 N A:GLY304 4.6 36.3 1.0 C A:LEU179 4.7 40.4 1.0 CA A:LEU179 4.7 40.0 1.0 CE2 A:TYR306 4.7 38.9 1.0 NE2 A:HIS143 4.8 36.6 1.0 C A:ASP178 5.0 39.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of HDAC8 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of HDAC8 in Complex with Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:42.6 occ:1.00 OD2 B:ASP267 2.0 46.3 1.0 OD1 B:ASP178 2.0 46.5 1.0 OAL B:C7401 2.0 54.6 1.0 OAK B:C7401 2.0 58.4 1.0 ND1 B:HIS180 2.1 46.6 1.0 CAI B:C7401 2.7 64.0 1.0 NAJ B:C7401 2.8 60.1 1.0 CG B:ASP178 2.8 43.8 1.0 OD2 B:ASP178 3.0 43.9 1.0 CE1 B:HIS180 3.0 47.1 1.0 CG B:ASP267 3.0 45.0 1.0 CG B:HIS180 3.1 45.1 1.0 OD1 B:ASP267 3.4 46.1 1.0 CB B:HIS180 3.5 43.9 1.0 N B:HIS180 3.8 42.4 1.0 NE2 B:HIS180 4.1 46.5 1.0 CD2 B:HIS180 4.2 45.1 1.0 CAH B:C7401 4.2 70.0 1.0 CB B:ASP178 4.3 43.3 1.0 N B:LEU179 4.3 42.8 1.0 CA B:HIS180 4.3 42.8 1.0 CA B:GLY304 4.3 42.2 1.0 CB B:ASP267 4.3 44.5 1.0 NE2 B:HIS142 4.4 41.1 1.0 CB B:LEU179 4.5 42.4 1.0 N B:GLY304 4.7 42.0 1.0 CE1 B:HIS142 4.7 41.0 1.0 C B:LEU179 4.7 42.4 1.0 NE2 B:HIS143 4.7 40.3 1.0 OH B:TYR306 4.8 43.2 1.0 CA B:LEU179 4.8 42.5 1.0 CE2 B:TYR306 4.9 43.0 1.0 C B:ASP178 4.9 43.0 1.0 CAG B:C7401 5.0 75.0 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of HDAC8 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of HDAC8 in Complex with Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:52.5 occ:1.00 OD2 C:ASP267 2.0 60.3 1.0 OAL C:C7401 2.0 62.0 1.0 OD1 C:ASP178 2.0 56.5 1.0 OAK C:C7401 2.0 65.8 1.0 ND1 C:HIS180 2.1 58.9 1.0 CAI C:C7401 2.7 72.6 1.0 NAJ C:C7401 2.8 67.8 1.0 CG C:ASP178 2.8 53.3 1.0 OD2 C:ASP178 2.8 53.9 1.0 CE1 C:HIS180 3.0 59.6 1.0 CG C:HIS180 3.1 57.8 1.0 CG C:ASP267 3.1 57.6 1.0 CB C:HIS180 3.5 55.8 1.0 OD1 C:ASP267 3.6 58.7 1.0 N C:HIS180 3.8 54.0 1.0 NE2 C:HIS180 4.1 59.3 1.0 CD2 C:HIS180 4.2 58.4 1.0 CB C:ASP178 4.2 52.4 1.0 CA C:GLY304 4.2 49.5 1.0 CAH C:C7401 4.2 79.1 1.0 CA C:HIS180 4.3 54.9 1.0 NE2 C:HIS142 4.3 54.8 1.0 CB C:ASP267 4.4 56.9 1.0 N C:LEU179 4.4 52.3 1.0 CB C:LEU179 4.6 52.5 1.0 N C:GLY304 4.6 48.6 1.0 OH C:TYR306 4.7 54.8 1.0 CE1 C:HIS142 4.7 55.1 1.0 C C:LEU179 4.7 53.4 1.0 CE2 C:TYR306 4.8 54.2 1.0 CA C:LEU179 4.8 52.8 1.0 NE2 C:HIS143 4.8 56.1 1.0 CAG C:C7401 5.0 84.4 1.0

X.Zheng, C.Conti, J.Caravella, M.-M.Zablocki, K.Bair, N.Barczak, B.Han, D.Lancia Jr., C.Liu, M.Martin, P.Y.Ng, A.Rudnitskaya, J.J.Thomason, R.Garcia-Dancey, C.Hardy, J.Lahdenranta, C.Leng, P.Li, E.Pardo, A.Saldahna, T.Tan, A.V.Toms, L.Yao, C.Zhang. Structure-Based Discovery of Novel N-(E)-N-Hydroxy-3-(2-(2-Oxoimidazolidin-1-Yl)Phenyl) Acrylamides As Potent and Selective HDAC8 Inhibitors To Be Published.